Britain has maintained a permanent diplomatic mission in Japan since 1859. The first legation was at Tozenji Temple in Edo, now called Tokyo, and the temple still stands today, not far from Shinagawa station. During the first thirteen years of the mission's history, diplomatic tensions and several attacks by disgruntled samurai forced a series of relocations: to Yokohama, Gotenyama, Sengakuji and finally to Yokohama again. The present site in front of the Imperial Palace at Ichiban-cho has been in use since 1872, when the then Minister, Sir Harry Parkes, insisted that the establishment be moved back from Yokohama to Tokyo, where much of the mission's work was concentrated. The site itself was provided as a mark of favour by the Meiji government and was leased to the British Government in perpetuity.

The original red brick buildings of the Embassy were completely destroyed in the great Kanto earthquake of 1923, forcing staff to live and work in temporary wooden structures until the Ambassador's Residence, the Chancery (the main office building) and the other structures were completed in 1929. These still stand today. A second office building, formally named 'the Annexe' but generally known as 'the New Building', was added in 1987.

During the Second World War, the British staff left the Embassy, but many of the Japanese staff remained resident. Despite several of the trees catching fire as a result of incendiaries falling nearby, the buildings and their contents survived relatively unscathed, thanks largely to the quick actions of these Japanese who stayed on the premises. Immediately after the war, the entire Embassy was commissioned as a ship of His Majesty's Navy - the H.M.S. Return - before being changed into a military establishment in May 1946. It was not until June of the same year, that the Embassy began to return to normal. It was known as the 'United Kingdom Liaison Mission in Japan' until the Japanese Peace Treaty of April 1952, when it finally acquired the official name of 'the British Embassy.'

The British Embassy is famous for its cherry tress, which are both inside and around the compound. The first cherry trees were planted in 1898 by the then Minister, Sir Ernest Satow, as a gift to the people of Tokyo and as a symbol of his love for Japan. They were replaced one hundred years later as part of Festival UK98, with the participation of Her Imperial Highness Princess Noriko. There are a number of other commemorative trees within the Embassy Compound, including an oak planted by Her Majesty The Queen in 1975, and another planted by Mrs Yoriko Kawaguchi, then Minister for the Environment and subsequently Minister for Foreign Affairs, to mark the start of the Green Alliance campaign in 2002.

Of the two memorials inside the Compound, one commemorates the fifty years of service of Miss Fuki Takeda, a Japanese servant of the Embassy; the other, those members of the Embassy staff who were killed in the First World War.